[maker-devel] failed contigs error report
Ian Misner
ianmisner at my.uri.edu
Fri Jul 12 04:47:39 MDT 2013
Hello,
I have collected my failed contigs and I have rerun them in Maker v. 2.28 but they have failed again. I don't know what the error codes mean but I have attached the run log for your review. Any help would be appreciated.
Cheers
Ian
-------------- next part --------------
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:
/home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore
To access files for individual sequences use the datastore index:
/home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_master_datastore_index.log
STATUS: Now running MAKER...
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_593
Length: 2882
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0 -pa 6
#-------------------------------#
No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.all.rb
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/te_proteins%2Efasta.mpi.10.0
#-------------------------------#
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/te_proteins%2Efasta.mpi.10.1
#-------------------------------#
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/te_proteins%2Efasta.mpi.10.2
#-------------------------------#
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/te_proteins%2Efasta.mpi.10.3
#-------------------------------#
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/te_proteins%2Efasta.mpi.10.4
#-------------------------------#
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/te_proteins%2Efasta.mpi.10.5
#-------------------------------#
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/te_proteins%2Efasta.mpi.10.6
#-------------------------------#
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/te_proteins%2Efasta.mpi.10.7
#-------------------------------#
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/te_proteins%2Efasta.mpi.10.8
#-------------------------------#
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/te_proteins%2Efasta.mpi.10.9
#-------------------------------#
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_593.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_593.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_593.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_593.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_593.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_593.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/AG1-IA_China_Prot%2Efasta.mpi.10.0
#-------------------------------#
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/AG1-IA_China_Prot%2Efasta.mpi.10.1
#-------------------------------#
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/AG1-IA_China_Prot%2Efasta.mpi.10.2
#-------------------------------#
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/AG1-IA_China_Prot%2Efasta.mpi.10.3
#-------------------------------#
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/AG1-IA_China_Prot%2Efasta.mpi.10.4
#-------------------------------#
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/AG1-IA_China_Prot%2Efasta.mpi.10.5
#-------------------------------#
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/AG1-IA_China_Prot%2Efasta.mpi.10.6
#-------------------------------#
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/AG1-IA_China_Prot%2Efasta.mpi.10.7
#-------------------------------#
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/AG1-IA_China_Prot%2Efasta.mpi.10.8
#-------------------------------#
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/AG1-IA_China_Prot%2Efasta.mpi.10.9
#-------------------------------#
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443917043%7Cgb%7CELU37906%2E1%7C.for.650-2882.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.650-2882.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.650-2882.gi%7C443917043%7Cgb%7CELU37906%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
...processing 0 of 2
...processing 1 of 2
processing the chunk divide
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.
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
annotating transcripts
Making transcripts
...processing 0 of 1
...processing 0 of 2
...processing 1 of 2
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/3_0.849-2882.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/3_0.849-2882.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/3_0.849-2882.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/3_0.849-2882.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/3_0.849-2882.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/3_0.849-2882.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: undefined coordinates
Coding 0 173 + 0.200 . . . ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_593
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_593
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_1981
Length: 10563
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0 -pa 6
#-------------------------------#
No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.all.rb
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_1981.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_1981.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_1981.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_1981.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_1981.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_1981.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
in cluster::shadow_cluster...
sorting hits in shadow cluster...
j_size:2 current j:0
j_size:2 current j:1
...finished clustering.
deleted:1 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
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
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
in cluster::shadow_cluster...
sorting hits in shadow cluster...
j_size:1 current j:0
...finished clustering.
deleted:1 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:1 hits
collecting blastx reports
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.
polishing proteins
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443926460%7Cgb%7CELU45116%2E1%7C.for.1-1765.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.1-1765.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.1-1765.gi%7C443926460%7Cgb%7CELU45116%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443926461%7Cgb%7CELU45117%2E1%7C.for.1462-7346.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.1462-7346.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.1462-7346.gi%7C443926461%7Cgb%7CELU45117%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443912614%7Cgb%7CELU35926%2E1%7C.for.4446-5532.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.4446-5532.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.4446-5532.gi%7C443912614%7Cgb%7CELU35926%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443916327%7Cgb%7CELU37443%2E1%7C.for.1450-6472.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.1450-6472.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.1450-6472.gi%7C443916327%7Cgb%7CELU37443%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443912636%7Cgb%7CELU35932%2E1%7C.for.1832-6106.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.1832-6106.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.1832-6106.gi%7C443912636%7Cgb%7CELU35932%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443916324%7Cgb%7CELU37441%2E1%7C.for.1618-7085.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.1618-7085.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.1618-7085.gi%7C443916324%7Cgb%7CELU37441%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443926454%7Cgb%7CELU45111%2E1%7C.for.3156-7343.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.3156-7343.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.3156-7343.gi%7C443926454%7Cgb%7CELU45111%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443912965%7Cgb%7CELU36010%2E1%7C.for.1462-5499.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.1462-5499.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.1462-5499.gi%7C443912965%7Cgb%7CELU36010%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443926455%7Cgb%7CELU45112%2E1%7C.for.7818-9781.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.7818-9781.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.7818-9781.gi%7C443926455%7Cgb%7CELU45112%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 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
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 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
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:8 now processing 0
total clusters:8 now processing 0
total clusters:8 now processing 0
total clusters:8 now processing 0
...processing 0 of 2
...processing 1 of 2
total clusters:8 now processing 0
total clusters:8 now processing 0
total clusters:8 now processing 0
total clusters:8 now processing 0
...processing 0 of 2
...processing 1 of 2
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
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
...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
total clusters:4 now processing 0
in cluster::shadow_cluster...
...finished clustering.
annotating transcripts
Making transcripts
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/9_0.852-1622.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/9_0.852-1622.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/9_0.852-1622.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/9_0.852-1622.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/9_0.852-1622.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/9_0.852-1622.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/10_0.5290-6220.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/10_0.5290-6220.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/10_0.5290-6220.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/10_0.5290-6220.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/10_0.5290-6220.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/10_0.5290-6220.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
...processing 0 of 2
...processing 1 of 2
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/11_0.8017-9584.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/11_0.8017-9584.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/11_0.8017-9584.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/11_0.8017-9584.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/11_0.8017-9584.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/11_0.8017-9584.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
...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
...processing 9 of 14
...processing 10 of 14
...processing 11 of 14
...processing 12 of 14
...processing 13 of 14
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/12_0.0-7386.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/12_0.0-7386.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/12_0.0-7386.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/12_0.0-7386.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/12_0.0-7386.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/12_0.0-7386.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/13_0.8583-9424.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/13_0.8583-9424.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/13_0.8583-9424.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/13_0.8583-9424.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/13_0.8583-9424.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/13_0.8583-9424.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
...processing 0 of 1
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/14_0.9504-10563.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/14_0.9504-10563.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/14_0.9504-10563.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/14_0.9504-10563.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/14_0.9504-10563.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/14_0.9504-10563.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: undefined coordinates
Coding 0 109 + 0.200 . . . ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_1981
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_1981
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_3516
Length: 3272
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0 -pa 6
#-------------------------------#
No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.all.rb
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_3516.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_3516.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_3516.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_3516.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_3516.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_3516.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:2 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
in cluster::shadow_cluster...
sorting hits in shadow cluster...
j_size:2 current j:0
j_size:2 current j:1
...finished clustering.
polishing proteins
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443924210%7Cgb%7CELU43269%2E1%7C.for.1-1171.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.1-1171.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.1-1171.gi%7C443924210%7Cgb%7CELU43269%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443926803%7Cgb%7CELU45366%2E1%7C.for.1-1446.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.1-1446.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.1-1446.gi%7C443926803%7Cgb%7CELU45366%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443926802%7Cgb%7CELU45365%2E1%7C.for.1965-3272.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.1965-3272.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.1965-3272.gi%7C443926802%7Cgb%7CELU45365%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
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 the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
...processing 0 of 1
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.2052-3272.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.2052-3272.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.2052-3272.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.2052-3272.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/4_0.2052-3272.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.2052-3272.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding -5 216 + 0.200 . . . ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_3516
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_3516
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_3821
Length: 7594
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0 -pa 6
#-------------------------------#
No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.all.rb
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_3821.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_3821.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_3821.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_3821.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_3821.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_3821.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443922723%7Cgb%7CELU42120%2E1%7C.for.2325-6375.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.2325-6375.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.2325-6375.gi%7C443922723%7Cgb%7CELU42120%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:7 now processing 0
...processing 0 of 2
...processing 1 of 2
total clusters:7 now processing 0
...processing 0 of 2
...processing 1 of 2
total clusters:7 now processing 0
...processing 0 of 2
...processing 1 of 2
total clusters:7 now processing 0
total clusters:7 now processing 0
...processing 0 of 2
...processing 1 of 2
total clusters:7 now processing 0
total clusters:7 now processing 0
...processing 0 of 2
...processing 1 of 2
processing the chunk divide
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
...processing 0 of 2
...processing 1 of 2
total clusters:3 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
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
total clusters:4 now processing 0
...processing 0 of 2
...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
annotating transcripts
Making transcripts
...processing 0 of 1
...processing 0 of 2
...processing 1 of 2
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.1478-6315.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.1478-6315.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.1478-6315.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.1478-6315.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/4_0.1478-6315.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.1478-6315.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
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.
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_4802
Length: 7225
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0 -pa 6
#-------------------------------#
No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.all.rb
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_4802.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_4802.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_4802.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_4802.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_4802.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_4802.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443914461%7Cgb%7CELU36415%2E1%7C.for.5310-7225.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.5310-7225.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.5310-7225.gi%7C443914461%7Cgb%7CELU36415%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
...processing 0 of 2
...processing 1 of 2
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.5497-7225.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.5497-7225.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.5497-7225.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.5497-7225.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/4_0.5497-7225.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.5497-7225.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
in cluster::shadow_cluster...
sorting hits in shadow cluster...
j_size:1 current j:0
...finished clustering.
...processing 0 of 2
...processing 1 of 2
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_4885
Length: 2762
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0 -pa 6
#-------------------------------#
No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.all.rb
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_4885.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_4885.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_4885.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_4885.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_4885.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_4885.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443925371%7Cgb%7CELU44224%2E1%7C.for.1-1052.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.1-1052.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.1-1052.gi%7C443925371%7Cgb%7CELU44224%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
...processing 0 of 2
...processing 1 of 2
processing the chunk divide
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.
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.
annotating transcripts
Making transcripts
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.559-1302.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.559-1302.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.559-1302.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.559-1302.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/2_0.559-1302.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.559-1302.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/3_0.2274-2762.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/3_0.2274-2762.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/3_0.2274-2762.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/3_0.2274-2762.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/3_0.2274-2762.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/3_0.2274-2762.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding10.20.30.40.50.60.70.80.90100 done
deleted:0 genes
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.548-1284.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.548-1284.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.548-1284.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.548-1284.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/4_0.548-1284.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.548-1284.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
...processing 0 of 1
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/5_0.2265-2762.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/5_0.2265-2762.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/5_0.2265-2762.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/5_0.2265-2762.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/5_0.2265-2762.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/5_0.2265-2762.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding10.20.30.40.50.60.70.80.90100 done
deleted:0 genes
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
processing chunk output
processing contig output
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_6364
Length: 6168
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0 -pa 6
#-------------------------------#
No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.all.rb
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_6364.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_6364.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_6364.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_6364.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_6364.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_6364.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:3 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:4 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:3 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:3 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:4 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:2 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:4 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:2 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
in cluster::shadow_cluster...
sorting hits in shadow cluster...
j_size:2 current j:0
j_size:2 current j:1
...finished clustering.
deleted:1 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:2 hits
collecting blastx reports
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.
polishing proteins
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443925319%7Cgb%7CELU44178%2E1%7C.for.1-1315.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.1-1315.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.1-1315.gi%7C443925319%7Cgb%7CELU44178%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443923087%7Cgb%7CELU42401%2E1%7C.for.1-1712.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.1-1712.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.1-1712.gi%7C443923087%7Cgb%7CELU42401%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443916516%7Cgb%7CELU37570%2E1%7C.for.1-1705.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.1-1705.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.1-1705.gi%7C443916516%7Cgb%7CELU37570%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443916517%7Cgb%7CELU37571%2E1%7C.for.1422-2768.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.1422-2768.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.1422-2768.gi%7C443916517%7Cgb%7CELU37571%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443916518%7Cgb%7CELU37572%2E1%7C.for.2243-6168.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.2243-6168.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.2243-6168.gi%7C443916518%7Cgb%7CELU37572%2E1%7C.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 3
...processing 1 of 3
...processing 2 of 3
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
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:6 now processing 0
total clusters:6 now processing 0
total clusters:6 now processing 0
total clusters:6 now processing 0
total clusters:6 now processing 0
total clusters:6 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
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
...processing 0 of 2
...processing 1 of 2
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
in cluster::shadow_cluster...
...finished clustering.
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.
annotating transcripts
Making transcripts
...processing 0 of 5
...processing 1 of 5
...processing 2 of 5
...processing 3 of 5
...processing 4 of 5
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.0-1530.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.0-1530.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.0-1530.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.0-1530.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/4_0.0-1530.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.0-1530.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
...processing 0 of 1
...processing 0 of 4
...processing 1 of 4
...processing 2 of 4
...processing 3 of 4
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/5_0.1618-6168.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/5_0.1618-6168.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/5_0.1618-6168.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/5_0.1618-6168.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/5_0.1618-6168.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/5_0.1618-6168.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: undefined coordinates
Coding 0 313 + 0.200 . . . ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_6364
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_6364
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_6661
Length: 5237
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0 -pa 6
#-------------------------------#
No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.all.rb
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_6661.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_6661.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_6661.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_6661.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_6661.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_6661.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
in cluster::shadow_cluster...
sorting hits in shadow cluster...
j_size:2 current j:0
j_size:2 current j:1
...finished clustering.
polishing proteins
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443919777%7Cgb%7CELU39849%2E1%7C.for.1-1825.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.1-1825.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.1-1825.gi%7C443919777%7Cgb%7CELU39849%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443919779%7Cgb%7CELU39851%2E1%7C.for.4180-5237.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.4180-5237.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.4180-5237.gi%7C443919779%7Cgb%7CELU39851%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
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 the chunk divide
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.
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.
annotating transcripts
Making transcripts
...processing 0 of 1
...processing 0 of 2
...processing 1 of 2
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/6_0.4281-5237.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/6_0.4281-5237.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/6_0.4281-5237.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/6_0.4281-5237.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/6_0.4281-5237.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/6_0.4281-5237.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
...processing 0 of 1
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/7_0.0-1662.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/7_0.0-1662.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/7_0.0-1662.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/7_0.0-1662.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/7_0.0-1662.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/7_0.0-1662.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Calling translate without a seq argument!
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:472
STACK: Bio::Tools::CodonTable::translate /usr/local/share/perl5/Bio/Tools/CodonTable.pm:411
STACK: PhatHit_utils::_adjust /home/ian_usda/Programs/maker_v2.28/bin/../lib/PhatHit_utils.pm:838
STACK: PhatHit_utils::adjust_start_stop /home/ian_usda/Programs/maker_v2.28/bin/../lib/PhatHit_utils.pm:786
STACK: maker::auto_annotator::load_transcript_struct /home/ian_usda/Programs/maker_v2.28/bin/../lib/maker/auto_annotator.pm:2086
STACK: maker::auto_annotator::group_transcripts /home/ian_usda/Programs/maker_v2.28/bin/../lib/maker/auto_annotator.pm:2495
STACK: maker::auto_annotator::annotate_genes /home/ian_usda/Programs/maker_v2.28/bin/../lib/maker/auto_annotator.pm:925
STACK: Process::MpiChunk::_go /home/ian_usda/Programs/maker_v2.28/bin/../lib/Process/MpiChunk.pm:3798
STACK: Process::MpiChunk::run /home/ian_usda/Programs/maker_v2.28/bin/../lib/Process/MpiChunk.pm:341
STACK: Process::MpiChunk::run_all /home/ian_usda/Programs/maker_v2.28/bin/../lib/Process/MpiChunk.pm:357
STACK: Process::MpiTiers::run_all /home/ian_usda/Programs/maker_v2.28/bin/../lib/Process/MpiTiers.pm:286
STACK: Process::MpiTiers::run_all /home/ian_usda/Programs/maker_v2.28/bin/../lib/Process/MpiTiers.pm:286
STACK: /home/ian_usda/Programs/maker_v2.28/bin/maker_v2.28:667
-----------------------------------------------------------
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while clustering transcripts into genes for annotations
ERROR: Chunk failed at level:2, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_6661
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_6661
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_7259
Length: 2706
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0 -pa 6
#-------------------------------#
No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.all.rb
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_7259.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_7259.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_7259.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_7259.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_7259.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_7259.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443919366%7Cgb%7CELU39560%2E1%7C.for.701-2706.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.701-2706.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.701-2706.gi%7C443919366%7Cgb%7CELU39560%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
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 the chunk divide
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.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
...processing 0 of 2
...processing 1 of 2
annotating transcripts
Making transcripts
...processing 0 of 1
...processing 0 of 2
...processing 1 of 2
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.897-2706.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.897-2706.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.897-2706.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.897-2706.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/2_0.897-2706.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.897-2706.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding -7 93 + 0.200 . . . ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_7259
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_7259
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_7484
Length: 4350
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0 -pa 6
#-------------------------------#
No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.all.rb
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_7484.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_7484.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_7484.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_7484.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_7484.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_7484.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
in cluster::shadow_cluster...
sorting hits in shadow cluster...
j_size:1 current j:0
...finished clustering.
polishing proteins
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443925858%7Cgb%7CELU44619%2E1%7C.for.3225-4350.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.3225-4350.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.3225-4350.gi%7C443925858%7Cgb%7CELU44619%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443926070%7Cgb%7CELU44813%2E1%7C.for.1-4350.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.1-4350.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.1-4350.gi%7C443926070%7Cgb%7CELU44813%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443918793%7Cgb%7CELU39161%2E1%7C.for.3207-4350.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.3207-4350.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.3207-4350.gi%7C443918793%7Cgb%7CELU39161%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:6 now processing 0
total clusters:6 now processing 0
total clusters:6 now processing 0
total clusters:6 now processing 0
total clusters:6 now processing 0
...processing 0 of 2
...processing 1 of 2
total clusters:6 now processing 0
processing the chunk divide
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.
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
annotating transcripts
Making transcripts
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/5_0.1394-2233.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/5_0.1394-2233.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/5_0.1394-2233.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/5_0.1394-2233.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/5_0.1394-2233.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/5_0.1394-2233.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
...processing 0 of 1
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/6_0.0-4350.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/6_0.0-4350.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/6_0.0-4350.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/6_0.0-4350.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/6_0.0-4350.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/6_0.0-4350.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding -7 195 + 0.200 . . . ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_7484
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_7484
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_7871
Length: 3828
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0 -pa 6
#-------------------------------#
No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.all.rb
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_7871.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_7871.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_7871.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_7871.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_7871.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_7871.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
in cluster::shadow_cluster...
sorting hits in shadow cluster...
j_size:1 current j:0
...finished clustering.
polishing proteins
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443915640%7Cgb%7CELU37016%2E1%7C.for.1-719.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.1-719.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.1-719.gi%7C443915640%7Cgb%7CELU37016%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443925409%7Cgb%7CELU44250%2E1%7C.for.1-719.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.1-719.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.1-719.gi%7C443925409%7Cgb%7CELU44250%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:5 now processing 0
total clusters:5 now processing 0
...processing 0 of 3
...processing 1 of 3
...processing 2 of 3
total clusters:5 now processing 0
total clusters:5 now processing 0
total clusters:5 now processing 0
processing the chunk divide
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 3
...processing 1 of 3
...processing 2 of 3
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
total clusters:3 now processing 0
in cluster::shadow_cluster...
...finished clustering.
annotating transcripts
Making transcripts
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/3_0.0-920.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/3_0.0-920.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/3_0.0-920.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/3_0.0-920.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/3_0.0-920.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/3_0.0-920.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.0-942.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.0-942.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.0-942.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.0-942.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/4_0.0-942.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.0-942.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
...processing 0 of 1
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/5_0.1513-3828.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/5_0.1513-3828.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/5_0.1513-3828.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/5_0.1513-3828.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/5_0.1513-3828.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/5_0.1513-3828.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
in cluster::shadow_cluster...
sorting hits in shadow cluster...
j_size:1 current j:0
...finished clustering.
...processing 0 of 2
...processing 1 of 2
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_12295
Length: 2576
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0 -pa 6
#-------------------------------#
No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.all.rb
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_12295.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_12295.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_12295.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_12295.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_12295.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_12295.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443920586%7Cgb%7CELU40485%2E1%7C.for.1-2576.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.1-2576.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.1-2576.gi%7C443920586%7Cgb%7CELU40485%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
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 the chunk divide
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.
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
annotating transcripts
Making transcripts
...processing 0 of 1
...processing 0 of 2
...processing 1 of 2
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-2576.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-2576.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-2576.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-2576.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/2_0.0-2576.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-2576.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding -2 194 + 0.200 . . . ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_12295
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_12295
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_12395
Length: 2252
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0 -pa 6
#-------------------------------#
No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.all.rb
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_12395.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_12395.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_12395.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_12395.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_12395.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_12395.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:2 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
in cluster::shadow_cluster...
sorting hits in shadow cluster...
j_size:1 current j:0
...finished clustering.
polishing proteins
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443915594%7Cgb%7CELU36979%2E1%7C.for.1-2252.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.1-2252.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.1-2252.gi%7C443915594%7Cgb%7CELU36979%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443915591%7Cgb%7CELU36976%2E1%7C.for.1-2252.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.1-2252.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.1-2252.gi%7C443915591%7Cgb%7CELU36976%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443926575%7Cgb%7CELU45191%2E1%7C.for.1373-2252.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.1373-2252.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.1373-2252.gi%7C443926575%7Cgb%7CELU45191%2E1%7C.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
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
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
annotating transcripts
Making transcripts
...processing 0 of 1
...processing 0 of 3
...processing 1 of 3
...processing 2 of 3
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.0-2252.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.0-2252.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.0-2252.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.0-2252.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/4_0.0-2252.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.0-2252.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: undefined coordinates
Coding 0 494 + 0.200 . . . ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_12395
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_12395
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_13247
Length: 1216
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0 -pa 6
#-------------------------------#
No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.all.rb
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_13247.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_13247.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_13247.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_13247.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_13247.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_13247.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:2 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443926761%7Cgb%7CELU45333%2E1%7C.for.1-1216.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.1-1216.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.1-1216.gi%7C443926761%7Cgb%7CELU45333%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk: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
processing the chunk divide
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
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.34-1216.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.34-1216.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.34-1216.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.34-1216.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/2_0.34-1216.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.34-1216.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
...processing 0 of 1
...processing 0 of 2
...processing 1 of 2
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/3_0.0-1216.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/3_0.0-1216.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/3_0.0-1216.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/3_0.0-1216.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/3_0.0-1216.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/3_0.0-1216.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding ... 782 + 0.200 . . . ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_13247
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_13247
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_14991
Length: 6593
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0 -pa 6
#-------------------------------#
No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.all.rb
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_14991.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_14991.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_14991.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_14991.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_14991.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_14991.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
in cluster::shadow_cluster...
sorting hits in shadow cluster...
j_size:2 current j:0
j_size:2 current j:1
...finished clustering.
polishing proteins
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443926230%7Cgb%7CELU44941%2E1%7C.for.1-813.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.1-813.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.1-813.gi%7C443926230%7Cgb%7CELU44941%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443926228%7Cgb%7CELU44939%2E1%7C.for.5427-6593.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.5427-6593.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.5427-6593.gi%7C443926228%7Cgb%7CELU44939%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:6 now processing 0
...processing 0 of 2
...processing 1 of 2
total clusters:6 now processing 0
total clusters:6 now processing 0
total clusters:6 now processing 0
...processing 0 of 2
...processing 1 of 2
total clusters:6 now processing 0
...processing 0 of 2
...processing 1 of 2
total clusters:6 now processing 0
processing the chunk divide
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 2
...processing 1 of 2
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
total clusters:3 now processing 0
...processing 0 of 2
...processing 1 of 2
total clusters:3 now processing 0
in cluster::shadow_cluster...
...finished clustering.
annotating transcripts
Making transcripts
...processing 0 of 1
...processing 0 of 2
...processing 1 of 2
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/5_0.0-653.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/5_0.0-653.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/5_0.0-653.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/5_0.0-653.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/5_0.0-653.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/5_0.0-653.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding10.20.30.40.50.60.70.80.90100 done
deleted:0 genes
...processing 0 of 1
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/6_0.5581-6593.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/6_0.5581-6593.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/6_0.5581-6593.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/6_0.5581-6593.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/6_0.5581-6593.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/6_0.5581-6593.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding -2 201 + 0.200 . . . ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_14991
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_14991
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_17930
Length: 1764
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0 -pa 6
#-------------------------------#
No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.all.rb
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_17930.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_17930.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_17930.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_17930.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_17930.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_17930.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443918707%7Cgb%7CELU39101%2E1%7C.for.1-1581.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.1-1581.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.1-1581.gi%7C443918707%7Cgb%7CELU39101%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
...processing 0 of 1
...processing 0 of 2
...processing 1 of 2
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.106-1764.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.106-1764.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.106-1764.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.106-1764.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/2_0.106-1764.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.106-1764.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding ... 967 + 0.200 . . . ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_17930
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_17930
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_18181
Length: 1918
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0 -pa 6
#-------------------------------#
No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.all.rb
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_18181.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_18181.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_18181.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_18181.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_18181.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_18181.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:1 hits
collecting blastx reports
polishing proteins
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443920490%7Cgb%7CELU40399%2E1%7C.for.1-933.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.1-933.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.1-933.gi%7C443920490%7Cgb%7CELU40399%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
processing the chunk divide
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.
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.
annotating transcripts
Making transcripts
...processing 0 of 1
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.965-1918.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.965-1918.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.965-1918.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.965-1918.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/4_0.965-1918.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.965-1918.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding -6 166 + 0.200 . . . ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_18181
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_18181
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_18734
Length: 1555
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0 -pa 6
#-------------------------------#
No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.all.rb
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_18734.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_18734.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_18734.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_18734.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_18734.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_18734.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:4 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:4 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:5 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:7 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:6 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:5 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
in cluster::shadow_cluster...
sorting hits in shadow cluster...
j_size:1 current j:0
...finished clustering.
deleted:6 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:5 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:1 hits
collecting blastx reports
in cluster::shadow_cluster...
sorting hits in shadow cluster...
j_size:1 current j:0
...finished clustering.
polishing proteins
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443915003%7Cgb%7CELU36646%2E1%7C.for.1-1555.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-1555.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-1555.gi%7C443915003%7Cgb%7CELU36646%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443921070%7Cgb%7CELU40845%2E1%7C.for.1-1555.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-1555.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-1555.gi%7C443921070%7Cgb%7CELU40845%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443915001%7Cgb%7CELU36644%2E1%7C.for.1-1507.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-1507.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-1507.gi%7C443915001%7Cgb%7CELU36644%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443923632%7Cgb%7CELU42812%2E1%7C.for.1-1555.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-1555.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-1555.gi%7C443923632%7Cgb%7CELU42812%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443915695%7Cgb%7CELU37052%2E1%7C.for.1-1555.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-1555.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-1555.gi%7C443915695%7Cgb%7CELU37052%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443924765%7Cgb%7CELU43732%2E1%7C.for.1-976.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-976.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-976.gi%7C443924765%7Cgb%7CELU43732%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443917077%7Cgb%7CELU37931%2E1%7C.for.1-838.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-838.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-838.gi%7C443917077%7Cgb%7CELU37931%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443916648%7Cgb%7CELU37640%2E1%7C.for.1-1555.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-1555.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-1555.gi%7C443916648%7Cgb%7CELU37640%2E1%7C.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 4
...processing 1 of 4
...processing 2 of 4
...processing 3 of 4
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
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 the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
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 4
...processing 1 of 4
...processing 2 of 4
...processing 3 of 4
...processing 0 of 2
...processing 1 of 2
...processing 0 of 4
...processing 1 of 4
...processing 2 of 4
...processing 3 of 4
annotating transcripts
Making transcripts
...processing 0 of 1
...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 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1555.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1555.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1555.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1555.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/2_0.0-1555.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1555.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
in cluster::shadow_cluster...
sorting hits in shadow cluster...
j_size:1 current j:0
...finished clustering.
...processing 0 of 5
...processing 1 of 5
...processing 2 of 5
...processing 3 of 5
...processing 4 of 5
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_19042
Length: 1697
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0 -pa 6
#-------------------------------#
No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.all.rb
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_19042.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_19042.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_19042.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_19042.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_19042.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_19042.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:2 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443926334%7Cgb%7CELU45026%2E1%7C.for.1-1697.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.1-1697.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.1-1697.gi%7C443926334%7Cgb%7CELU45026%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
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 the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
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
annotating transcripts
Making transcripts
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1697.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1697.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1697.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1697.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/2_0.0-1697.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1697.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/3_0.0-1697.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/3_0.0-1697.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/3_0.0-1697.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/3_0.0-1697.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/3_0.0-1697.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/3_0.0-1697.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
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
processing chunk output
processing contig output
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_19068
Length: 1079
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0 -pa 6
#-------------------------------#
No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.all.rb
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_19068.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_19068.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_19068.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_19068.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_19068.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_19068.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443920586%7Cgb%7CELU40485%2E1%7C.for.1-1079.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.1-1079.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.1-1079.gi%7C443920586%7Cgb%7CELU40485%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
...processing 0 of 1
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1079.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1079.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1079.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1079.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/2_0.0-1079.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1079.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding -4 179 + 0.200 . . . ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_19068
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_19068
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_19560
Length: 1347
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0 -pa 6
#-------------------------------#
No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.all.rb
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_19560.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_19560.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_19560.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_19560.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_19560.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_19560.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1347.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1347.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1347.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1347.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/2_0.0-1347.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1347.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/3_0.0-1347.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/3_0.0-1347.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/3_0.0-1347.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/3_0.0-1347.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/3_0.0-1347.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/3_0.0-1347.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
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
processing chunk output
processing contig output
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_20762
Length: 1062
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0 -pa 6
#-------------------------------#
No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.all.rb
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_20762.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_20762.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_20762.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_20762.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_20762.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_20762.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443924504%7Cgb%7CELU43508%2E1%7C.for.1-982.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.1-982.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.1-982.gi%7C443924504%7Cgb%7CELU43508%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
processing the chunk divide
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
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
...processing 0 of 2
...processing 1 of 2
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1062.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1062.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1062.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1062.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/2_0.0-1062.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1062.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
...processing 0 of 1
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/3_0.504-1062.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/3_0.504-1062.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/3_0.504-1062.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/3_0.504-1062.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/3_0.504-1062.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/3_0.504-1062.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding -5 154 + 0.200 . . . ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_20762
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_20762
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_20773
Length: 1596
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0 -pa 6
#-------------------------------#
No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.all.rb
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_20773.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_20773.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_20773.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_20773.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_20773.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_20773.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443923085%7Cgb%7CELU42399%2E1%7C.for.76-1596.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.76-1596.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.76-1596.gi%7C443923085%7Cgb%7CELU42399%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
processing the chunk divide
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.
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.
annotating transcripts
Making transcripts
...processing 0 of 1
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.269-1596.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.269-1596.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.269-1596.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.269-1596.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/2_0.269-1596.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.269-1596.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding -5 228 + 0.200 . . . ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_20773
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_20773
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_21166
Length: 2541
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0 -pa 6
#-------------------------------#
No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.all.rb
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_21166.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_21166.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_21166.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_21166.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_21166.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_21166.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443912610%7Cgb%7CELU35925%2E1%7C.for.1700-2541.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.1700-2541.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.1700-2541.gi%7C443912610%7Cgb%7CELU35925%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk: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
processing the chunk divide
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.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
...processing 0 of 1
...processing 0 of 2
...processing 1 of 2
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.1569-2541.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.1569-2541.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.1569-2541.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.1569-2541.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/4_0.1569-2541.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.1569-2541.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
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
processing chunk output
processing contig output
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_21504
Length: 1823
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0 -pa 6
#-------------------------------#
No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.all.rb
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_21504.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_21504.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_21504.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_21504.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_21504.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_21504.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443917001%7Cgb%7CELU37876%2E1%7C.for.1-1497.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.1-1497.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.1-1497.gi%7C443917001%7Cgb%7CELU37876%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
...processing 0 of 1
...processing 0 of 2
...processing 1 of 2
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1823.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1823.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1823.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1823.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/2_0.0-1823.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1823.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: undefined coordinates
Coding 0 1025 + 0.200 . . . ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_21504
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_21504
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_21572
Length: 1139
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0 -pa 6
#-------------------------------#
No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.all.rb
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_21572.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_21572.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_21572.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_21572.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_21572.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_21572.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443918865%7Cgb%7CELU39212%2E1%7C.for.1-1139.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.1-1139.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.1-1139.gi%7C443918865%7Cgb%7CELU39212%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
...processing 0 of 1
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1139.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1139.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1139.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1139.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/2_0.0-1139.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1139.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: undefined coordinates
Coding 0 760 + 0.200 . . . ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_21572
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_21572
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_22153
Length: 1068
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0 -pa 6
#-------------------------------#
No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.all.rb
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_22153.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_22153.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_22153.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_22153.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_22153.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_22153.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
...processing 0 of 1
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1068.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1068.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1068.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1068.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/2_0.0-1068.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1068.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding -7 295 + 0.200 . . . ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_22153
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_22153
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_23198
Length: 2379
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0 -pa 6
#-------------------------------#
No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.all.rb
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_23198.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_23198.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_23198.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_23198.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_23198.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_23198.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443915448%7Cgb%7CELU36902%2E1%7C.for.1-2379.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.1-2379.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.1-2379.gi%7C443915448%7Cgb%7CELU36902%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
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
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
...processing 0 of 2
...processing 1 of 2
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-2379.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-2379.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-2379.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-2379.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/2_0.0-2379.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-2379.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
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
processing chunk output
processing contig output
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_23332
Length: 1024
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0 -pa 6
#-------------------------------#
No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.all.rb
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_23332.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_23332.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_23332.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_23332.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_23332.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_23332.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443924676%7Cgb%7CELU43665%2E1%7C.for.1-1024.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.1-1024.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.1-1024.gi%7C443924676%7Cgb%7CELU43665%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1024.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1024.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1024.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1024.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/2_0.0-1024.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1024.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
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
processing chunk output
processing contig output
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_24240
Length: 1060
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0 -pa 6
#-------------------------------#
No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.all.rb
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_24240.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_24240.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_24240.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_24240.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_24240.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_24240.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1060.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1060.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1060.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1060.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/2_0.0-1060.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1060.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/3_0.0-1060.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/3_0.0-1060.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/3_0.0-1060.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/3_0.0-1060.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/3_0.0-1060.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/3_0.0-1060.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
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
processing chunk output
processing contig output
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_26300
Length: 1034
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0 -pa 6
#-------------------------------#
No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.all.rb
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_26300.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_26300.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_26300.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_26300.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_26300.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_26300.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
annotating transcripts
Making transcripts
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
processing chunk output
processing contig output
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_26955
Length: 1407
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0 -pa 6
#-------------------------------#
No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.all.rb
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_26955.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_26955.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_26955.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_26955.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_26955.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_26955.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
in cluster::shadow_cluster...
sorting hits in shadow cluster...
j_size:1 current j:0
...finished clustering.
polishing proteins
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443917806%7Cgb%7CELU38443%2E1%7C.for.379-1407.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.379-1407.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.379-1407.gi%7C443917806%7Cgb%7CELU38443%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443917814%7Cgb%7CELU38450%2E1%7C.for.442-1407.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.442-1407.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.442-1407.gi%7C443917814%7Cgb%7CELU38450%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
annotating transcripts
Making transcripts
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
processing chunk output
processing contig output
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_27128
Length: 2040
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0 -pa 6
#-------------------------------#
No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.all.rb
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_27128.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_27128.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_27128.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_27128.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_27128.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_27128.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
in cluster::shadow_cluster...
sorting hits in shadow cluster...
j_size:2 current j:0
j_size:2 current j:1
...finished clustering.
polishing proteins
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443919020%7Cgb%7CELU39318%2E1%7C.for.1-941.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.1-941.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.1-941.gi%7C443919020%7Cgb%7CELU39318%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443923430%7Cgb%7CELU42674%2E1%7C.for.1-1055.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.1-1055.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.1-1055.gi%7C443923430%7Cgb%7CELU42674%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443927136%7Cgb%7CELU45660%2E1%7C.for.1096-2040.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.1096-2040.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.1096-2040.gi%7C443927136%7Cgb%7CELU45660%2E1%7C.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
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
processing the chunk divide
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
annotating transcripts
Making transcripts
...processing 0 of 3
...processing 1 of 3
...processing 2 of 3
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/3_0.0-2040.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/3_0.0-2040.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/3_0.0-2040.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/3_0.0-2040.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/3_0.0-2040.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/3_0.0-2040.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
in cluster::shadow_cluster...
sorting hits in shadow cluster...
j_size:1 current j:0
...finished clustering.
...processing 0 of 2
...processing 1 of 2
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_27180
Length: 1087
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0 -pa 6
#-------------------------------#
No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.all.rb
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_27180.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_27180.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_27180.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_27180.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_27180.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_27180.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443915961%7Cgb%7CELU37227%2E1%7C.for.1-1087.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.1-1087.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.1-1087.gi%7C443915961%7Cgb%7CELU37227%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
annotating transcripts
Making transcripts
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
processing chunk output
processing contig output
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_27507
Length: 2741
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0 -pa 6
#-------------------------------#
No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.all.rb
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_27507.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_27507.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_27507.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_27507.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_27507.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_27507.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
in cluster::shadow_cluster...
sorting hits in shadow cluster...
j_size:1 current j:0
...finished clustering.
deleted:1 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
in cluster::shadow_cluster...
sorting hits in shadow cluster...
j_size:1 current j:0
...finished clustering.
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
in cluster::shadow_cluster...
sorting hits in shadow cluster...
j_size:1 current j:0
...finished clustering.
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
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
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
in cluster::shadow_cluster...
sorting hits in shadow cluster...
j_size:1 current j:0
...finished clustering.
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
in cluster::shadow_cluster...
sorting hits in shadow cluster...
j_size:1 current j:0
...finished clustering.
deleted:2 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
in cluster::shadow_cluster...
sorting hits in shadow cluster...
j_size:1 current j:0
...finished clustering.
deleted:1 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
in cluster::shadow_cluster...
sorting hits in shadow cluster...
j_size:1 current j:0
...finished clustering.
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
in cluster::shadow_cluster...
sorting hits in shadow cluster...
j_size:1 current j:0
...finished clustering.
deleted:1 hits
collecting blastx reports
in cluster::shadow_cluster...
sorting hits in shadow cluster...
j_size:1 current j:0
...finished clustering.
polishing proteins
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443914358%7Cgb%7CELU36379%2E1%7C.for.1-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.gi%7C443914358%7Cgb%7CELU36379%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443912830%7Cgb%7CELU35979%2E1%7C.for.893-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.893-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.893-2741.gi%7C443912830%7Cgb%7CELU35979%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443918905%7Cgb%7CELU39238%2E1%7C.for.1-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.gi%7C443918905%7Cgb%7CELU39238%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443916513%7Cgb%7CELU37568%2E1%7C.for.1-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.gi%7C443916513%7Cgb%7CELU37568%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443915770%7Cgb%7CELU37108%2E1%7C.for.1-787.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-787.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-787.gi%7C443915770%7Cgb%7CELU37108%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443913539%7Cgb%7CELU36157%2E1%7C.for.869-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.869-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.869-2741.gi%7C443913539%7Cgb%7CELU36157%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443913039%7Cgb%7CELU36027%2E1%7C.for.890-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.890-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.890-2741.gi%7C443913039%7Cgb%7CELU36027%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443911450%7Cgb%7CELU35667%2E1%7C.for.893-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.893-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.893-2741.gi%7C443911450%7Cgb%7CELU35667%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443915845%7Cgb%7CELU37156%2E1%7C.for.1-793.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-793.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-793.gi%7C443915845%7Cgb%7CELU37156%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443915742%7Cgb%7CELU37086%2E1%7C.for.890-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.890-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.890-2741.gi%7C443915742%7Cgb%7CELU37086%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443924323%7Cgb%7CELU43365%2E1%7C.for.1-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.gi%7C443924323%7Cgb%7CELU43365%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443914832%7Cgb%7CELU36565%2E1%7C.for.893-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.893-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.893-2741.gi%7C443914832%7Cgb%7CELU36565%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443913337%7Cgb%7CELU36105%2E1%7C.for.893-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.893-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.893-2741.gi%7C443913337%7Cgb%7CELU36105%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443916857%7Cgb%7CELU37794%2E1%7C.for.1-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.gi%7C443916857%7Cgb%7CELU37794%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443915502%7Cgb%7CELU36924%2E1%7C.for.1-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.gi%7C443915502%7Cgb%7CELU36924%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443921084%7Cgb%7CELU40854%2E1%7C.for.1-799.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-799.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-799.gi%7C443921084%7Cgb%7CELU40854%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443915712%7Cgb%7CELU37064%2E1%7C.for.2201-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.2201-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.2201-2741.gi%7C443915712%7Cgb%7CELU37064%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443922842%7Cgb%7CELU42213%2E1%7C.for.1-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.gi%7C443922842%7Cgb%7CELU42213%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443918751%7Cgb%7CELU39123%2E1%7C.for.1-793.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-793.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-793.gi%7C443918751%7Cgb%7CELU39123%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443912860%7Cgb%7CELU35983%2E1%7C.for.869-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.869-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.869-2741.gi%7C443912860%7Cgb%7CELU35983%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443922901%7Cgb%7CELU42252%2E1%7C.for.1-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.gi%7C443922901%7Cgb%7CELU42252%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443913566%7Cgb%7CELU36162%2E1%7C.for.1157-2601.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1157-2601.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1157-2601.gi%7C443913566%7Cgb%7CELU36162%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443914292%7Cgb%7CELU36361%2E1%7C.for.893-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.893-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.893-2741.gi%7C443914292%7Cgb%7CELU36361%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443917664%7Cgb%7CELU38330%2E1%7C.for.1-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.gi%7C443917664%7Cgb%7CELU38330%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443921379%7Cgb%7CELU41050%2E1%7C.for.2069-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.2069-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.2069-2741.gi%7C443921379%7Cgb%7CELU41050%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 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
...processing 9 of 14
...processing 10 of 14
...processing 11 of 14
...processing 12 of 14
...processing 13 of 14
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
...processing 0 of 38
...processing 1 of 38
...processing 2 of 38
...processing 3 of 38
...processing 4 of 38
...processing 5 of 38
...processing 6 of 38
...processing 7 of 38
...processing 8 of 38
...processing 9 of 38
...processing 10 of 38
...processing 11 of 38
...processing 12 of 38
...processing 13 of 38
...processing 14 of 38
...processing 15 of 38
...processing 16 of 38
...processing 17 of 38
...processing 18 of 38
...processing 19 of 38
...processing 20 of 38
...processing 21 of 38
...trimming the rest
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
processing the chunk divide
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 22
...processing 1 of 22
...processing 2 of 22
...processing 3 of 22
...processing 4 of 22
...processing 5 of 22
...processing 6 of 22
...processing 7 of 22
...processing 8 of 22
...processing 9 of 22
...processing 10 of 22
...processing 11 of 22
...processing 12 of 22
...processing 13 of 22
...processing 14 of 22
...processing 15 of 22
...processing 16 of 22
...processing 17 of 22
...processing 18 of 22
...processing 19 of 22
...trimming the rest
...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
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
...processing 0 of 32
...processing 1 of 32
...processing 2 of 32
...processing 3 of 32
...processing 4 of 32
...processing 5 of 32
...processing 6 of 32
...processing 7 of 32
...processing 8 of 32
...processing 9 of 32
...processing 10 of 32
...processing 11 of 32
...processing 12 of 32
...processing 13 of 32
...processing 14 of 32
...processing 15 of 32
...processing 16 of 32
...processing 17 of 32
...processing 18 of 32
...processing 19 of 32
...processing 20 of 32
...processing 21 of 32
...processing 22 of 32
...processing 23 of 32
...processing 24 of 32
...processing 25 of 32
...processing 26 of 32
...processing 27 of 32
...processing 28 of 32
...processing 29 of 32
...processing 30 of 32
...processing 31 of 32
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.0-2741.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.0-2741.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.0-2741.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.0-2741.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/4_0.0-2741.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.0-2741.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/5_0.0-599.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/5_0.0-599.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/5_0.0-599.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/5_0.0-599.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/5_0.0-599.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/5_0.0-599.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
in cluster::shadow_cluster...
sorting hits in shadow cluster...
j_size:1 current j:0
...finished clustering.
...processing 0 of 20
...processing 1 of 20
...processing 2 of 20
...processing 3 of 20
...processing 4 of 20
...processing 5 of 20
...processing 6 of 20
...processing 7 of 20
...processing 8 of 20
...processing 9 of 20
...processing 10 of 20
...processing 11 of 20
...processing 12 of 20
...processing 13 of 20
...processing 14 of 20
...processing 15 of 20
...processing 16 of 20
...processing 17 of 20
...processing 18 of 20
...processing 19 of 20
in cluster::shadow_cluster...
sorting hits in shadow cluster...
j_size:2 current j:0
j_size:2 current j:1
...finished clustering.
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_28349
Length: 1535
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0 -pa 6
#-------------------------------#
No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.all.rb
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_28349.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_28349.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_28349.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_28349.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_28349.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_28349.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:1 hits
collecting blastx reports
in cluster::shadow_cluster...
sorting hits in shadow cluster...
j_size:1 current j:0
...finished clustering.
polishing proteins
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443926253%7Cgb%7CELU44961%2E1%7C.for.535-1535.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.535-1535.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.535-1535.gi%7C443926253%7Cgb%7CELU44961%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443921201%7Cgb%7CELU40930%2E1%7C.for.1-1427.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.1-1427.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.1-1427.gi%7C443921201%7Cgb%7CELU40930%2E1%7C.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
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
processing the chunk divide
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
annotating transcripts
Making transcripts
...processing 0 of 3
...processing 1 of 3
...processing 2 of 3
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1535.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1535.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1535.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1535.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/2_0.0-1535.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1535.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
in cluster::shadow_cluster...
sorting hits in shadow cluster...
j_size:2 current j:0
j_size:2 current j:1
...finished clustering.
in cluster::shadow_cluster...
sorting hits in shadow cluster...
j_size:1 current j:0
...finished clustering.
...processing 0 of 2
...processing 1 of 2
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_29160
Length: 1830
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0 -pa 6
#-------------------------------#
No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.all.rb
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_29160.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_29160.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_29160.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_29160.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_29160.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_29160.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
in cluster::shadow_cluster...
sorting hits in shadow cluster...
j_size:1 current j:0
...finished clustering.
polishing proteins
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443924283%7Cgb%7CELU43333%2E1%7C.for.652-1830.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.652-1830.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.652-1830.gi%7C443924283%7Cgb%7CELU43333%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443924238%7Cgb%7CELU43291%2E1%7C.for.589-1830.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.589-1830.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.589-1830.gi%7C443924238%7Cgb%7CELU43291%2E1%7C.p.exonerate
#-------------------------------#
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443924237%7Cgb%7CELU43290%2E1%7C.for.547-1830.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.547-1830.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.547-1830.gi%7C443924237%7Cgb%7CELU43290%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
processing the chunk divide
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
annotating transcripts
Making transcripts
...processing 0 of 2
...processing 1 of 2
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.743-1830.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.743-1830.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.743-1830.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.743-1830.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/2_0.743-1830.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.743-1830.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
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
processing chunk output
processing contig output
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_29352
Length: 1073
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0 -pa 6
#-------------------------------#
No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.all.rb
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_29352.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_29352.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_29352.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_29352.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_29352.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_29352.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443925337%7Cgb%7CELU44194%2E1%7C.for.1-1073.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.1-1073.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.1-1073.gi%7C443925337%7Cgb%7CELU44194%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
annotating transcripts
Making transcripts
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
processing chunk output
processing contig output
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_29511
Length: 1330
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0 -pa 6
#-------------------------------#
No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.all.rb
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_29511.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_29511.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_29511.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_29511.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_29511.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_29511.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443923460%7Cgb%7CELU42699%2E1%7C.for.1-1229.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.1-1229.0.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.1-1229.gi%7C443923460%7Cgb%7CELU42699%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
annotating transcripts
Making transcripts
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
processing chunk output
processing contig output
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_32665
Length: 1132
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0 -pa 6
#-------------------------------#
No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.all.rb
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.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:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_32665.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_32665.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_32665.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_32665.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_32665.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_32665.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
annotating transcripts
Making transcripts
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
processing chunk output
processing contig output
examining contents of the fasta file and run log
--Next Contig--
Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/3_0.849-2882.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_593
Length: 2882
Tries: 2!!
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
processing the chunk divide
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.
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
annotating transcripts
Making transcripts
...processing 0 of 1
...processing 0 of 2
...processing 1 of 2
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/3_0.849-2882.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/3_0.849-2882.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/3_0.849-2882.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/3_0.849-2882.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/3_0.849-2882.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/3_0.849-2882.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: undefined coordinates
Coding 0 173 + 0.200 . . . ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_593
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_593
examining contents of the fasta file and run log
--Next Contig--
Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/14_0.9504-10563.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_1981
Length: 10563
Tries: 2!!
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
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
...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
total clusters:4 now processing 0
in cluster::shadow_cluster...
...finished clustering.
annotating transcripts
Making transcripts
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/9_0.852-1622.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/9_0.852-1622.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/9_0.852-1622.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/9_0.852-1622.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/9_0.852-1622.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/9_0.852-1622.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/10_0.5290-6220.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/10_0.5290-6220.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/10_0.5290-6220.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/10_0.5290-6220.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/10_0.5290-6220.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/10_0.5290-6220.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
...processing 0 of 2
...processing 1 of 2
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/11_0.8017-9584.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/11_0.8017-9584.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/11_0.8017-9584.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/11_0.8017-9584.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/11_0.8017-9584.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/11_0.8017-9584.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
...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
...processing 9 of 14
...processing 10 of 14
...processing 11 of 14
...processing 12 of 14
...processing 13 of 14
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/12_0.0-7386.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/12_0.0-7386.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/12_0.0-7386.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/12_0.0-7386.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/12_0.0-7386.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/12_0.0-7386.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/13_0.8583-9424.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/13_0.8583-9424.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/13_0.8583-9424.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/13_0.8583-9424.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/13_0.8583-9424.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/13_0.8583-9424.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
...processing 0 of 1
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/14_0.9504-10563.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/14_0.9504-10563.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/14_0.9504-10563.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/14_0.9504-10563.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/14_0.9504-10563.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/14_0.9504-10563.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: undefined coordinates
Coding 0 109 + 0.200 . . . ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_1981
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_1981
examining contents of the fasta file and run log
--Next Contig--
Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/4_0.2052-3272.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_3516
Length: 3272
Tries: 2!!
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
...processing 0 of 1
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.2052-3272.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.2052-3272.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.2052-3272.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.2052-3272.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/4_0.2052-3272.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.2052-3272.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding -5 216 + 0.200 . . . ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_3516
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_3516
examining contents of the fasta file and run log
--Next Contig--
Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/5_0.1618-6168.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_6364
Length: 6168
Tries: 2!!
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
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
...processing 0 of 2
...processing 1 of 2
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
in cluster::shadow_cluster...
...finished clustering.
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.
annotating transcripts
Making transcripts
...processing 0 of 5
...processing 1 of 5
...processing 2 of 5
...processing 3 of 5
...processing 4 of 5
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.0-1530.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.0-1530.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.0-1530.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.0-1530.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/4_0.0-1530.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.0-1530.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
...processing 0 of 1
...processing 0 of 4
...processing 1 of 4
...processing 2 of 4
...processing 3 of 4
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/5_0.1618-6168.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/5_0.1618-6168.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/5_0.1618-6168.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/5_0.1618-6168.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/5_0.1618-6168.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/5_0.1618-6168.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: undefined coordinates
Coding 0 313 + 0.200 . . . ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_6364
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_6364
examining contents of the fasta file and run log
--Next Contig--
Processing run.log file...
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_6661
Length: 5237
Tries: 2!!
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
processing the chunk divide
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.
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.
annotating transcripts
Making transcripts
...processing 0 of 1
...processing 0 of 2
...processing 1 of 2
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/6_0.4281-5237.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/6_0.4281-5237.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/6_0.4281-5237.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/6_0.4281-5237.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/6_0.4281-5237.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/6_0.4281-5237.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
...processing 0 of 1
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/7_0.0-1662.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/7_0.0-1662.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/7_0.0-1662.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/7_0.0-1662.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/7_0.0-1662.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/7_0.0-1662.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Calling translate without a seq argument!
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:472
STACK: Bio::Tools::CodonTable::translate /usr/local/share/perl5/Bio/Tools/CodonTable.pm:411
STACK: PhatHit_utils::_adjust /home/ian_usda/Programs/maker_v2.28/bin/../lib/PhatHit_utils.pm:838
STACK: PhatHit_utils::adjust_start_stop /home/ian_usda/Programs/maker_v2.28/bin/../lib/PhatHit_utils.pm:786
STACK: maker::auto_annotator::load_transcript_struct /home/ian_usda/Programs/maker_v2.28/bin/../lib/maker/auto_annotator.pm:2086
STACK: maker::auto_annotator::group_transcripts /home/ian_usda/Programs/maker_v2.28/bin/../lib/maker/auto_annotator.pm:2495
STACK: maker::auto_annotator::annotate_genes /home/ian_usda/Programs/maker_v2.28/bin/../lib/maker/auto_annotator.pm:925
STACK: Process::MpiChunk::_go /home/ian_usda/Programs/maker_v2.28/bin/../lib/Process/MpiChunk.pm:3798
STACK: Process::MpiChunk::run /home/ian_usda/Programs/maker_v2.28/bin/../lib/Process/MpiChunk.pm:341
STACK: Process::MpiChunk::run_all /home/ian_usda/Programs/maker_v2.28/bin/../lib/Process/MpiChunk.pm:357
STACK: Process::MpiTiers::run_all /home/ian_usda/Programs/maker_v2.28/bin/../lib/Process/MpiTiers.pm:286
STACK: Process::MpiTiers::run_all /home/ian_usda/Programs/maker_v2.28/bin/../lib/Process/MpiTiers.pm:286
STACK: /home/ian_usda/Programs/maker_v2.28/bin/maker_v2.28:667
-----------------------------------------------------------
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while clustering transcripts into genes for annotations
ERROR: Chunk failed at level:2, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_6661
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_6661
examining contents of the fasta file and run log
--Next Contig--
Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/2_0.897-2706.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_7259
Length: 2706
Tries: 2!!
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
processing the chunk divide
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.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
...processing 0 of 2
...processing 1 of 2
annotating transcripts
Making transcripts
...processing 0 of 1
...processing 0 of 2
...processing 1 of 2
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.897-2706.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.897-2706.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.897-2706.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.897-2706.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/2_0.897-2706.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.897-2706.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding -7 93 + 0.200 . . . ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_7259
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_7259
examining contents of the fasta file and run log
--Next Contig--
Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/6_0.0-4350.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_7484
Length: 4350
Tries: 2!!
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
processing the chunk divide
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.
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
annotating transcripts
Making transcripts
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/5_0.1394-2233.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/5_0.1394-2233.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/5_0.1394-2233.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/5_0.1394-2233.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/5_0.1394-2233.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/5_0.1394-2233.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
...processing 0 of 1
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/6_0.0-4350.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/6_0.0-4350.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/6_0.0-4350.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/6_0.0-4350.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/6_0.0-4350.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/6_0.0-4350.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding -7 195 + 0.200 . . . ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_7484
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_7484
examining contents of the fasta file and run log
--Next Contig--
Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/2_0.0-2576.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_12295
Length: 2576
Tries: 2!!
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
processing the chunk divide
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.
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
annotating transcripts
Making transcripts
...processing 0 of 1
...processing 0 of 2
...processing 1 of 2
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-2576.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-2576.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-2576.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-2576.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/2_0.0-2576.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-2576.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding -2 194 + 0.200 . . . ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_12295
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_12295
examining contents of the fasta file and run log
--Next Contig--
Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/4_0.0-2252.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_12395
Length: 2252
Tries: 2!!
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
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
annotating transcripts
Making transcripts
...processing 0 of 1
...processing 0 of 3
...processing 1 of 3
...processing 2 of 3
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.0-2252.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.0-2252.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.0-2252.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.0-2252.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/4_0.0-2252.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.0-2252.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: undefined coordinates
Coding 0 494 + 0.200 . . . ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_12395
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_12395
examining contents of the fasta file and run log
--Next Contig--
Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/3_0.0-1216.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_13247
Length: 1216
Tries: 2!!
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
processing the chunk divide
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
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.34-1216.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.34-1216.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.34-1216.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.34-1216.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/2_0.34-1216.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.34-1216.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
...processing 0 of 1
...processing 0 of 2
...processing 1 of 2
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/3_0.0-1216.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/3_0.0-1216.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/3_0.0-1216.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/3_0.0-1216.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/3_0.0-1216.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/3_0.0-1216.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding ... 782 + 0.200 . . . ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_13247
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_13247
examining contents of the fasta file and run log
--Next Contig--
Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/6_0.5581-6593.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_14991
Length: 6593
Tries: 2!!
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
processing the chunk divide
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 2
...processing 1 of 2
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
total clusters:3 now processing 0
...processing 0 of 2
...processing 1 of 2
total clusters:3 now processing 0
in cluster::shadow_cluster...
...finished clustering.
annotating transcripts
Making transcripts
...processing 0 of 1
...processing 0 of 2
...processing 1 of 2
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/5_0.0-653.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/5_0.0-653.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/5_0.0-653.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/5_0.0-653.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/5_0.0-653.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/5_0.0-653.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding10.20.30.40.50.60.70.80.90100 done
deleted:0 genes
...processing 0 of 1
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/6_0.5581-6593.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/6_0.5581-6593.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/6_0.5581-6593.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/6_0.5581-6593.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/6_0.5581-6593.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/6_0.5581-6593.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding -2 201 + 0.200 . . . ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_14991
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_14991
examining contents of the fasta file and run log
--Next Contig--
Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/2_0.106-1764.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_17930
Length: 1764
Tries: 2!!
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
...processing 0 of 1
...processing 0 of 2
...processing 1 of 2
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.106-1764.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.106-1764.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.106-1764.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.106-1764.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/2_0.106-1764.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.106-1764.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding ... 967 + 0.200 . . . ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_17930
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_17930
examining contents of the fasta file and run log
--Next Contig--
Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/4_0.965-1918.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_18181
Length: 1918
Tries: 2!!
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
processing the chunk divide
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.
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.
annotating transcripts
Making transcripts
...processing 0 of 1
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.965-1918.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.965-1918.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.965-1918.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.965-1918.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/4_0.965-1918.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.965-1918.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding -6 166 + 0.200 . . . ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_18181
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_18181
examining contents of the fasta file and run log
--Next Contig--
Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/2_0.0-1079.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_19068
Length: 1079
Tries: 2!!
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
...processing 0 of 1
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1079.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1079.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1079.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1079.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/2_0.0-1079.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1079.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding -4 179 + 0.200 . . . ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_19068
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_19068
examining contents of the fasta file and run log
--Next Contig--
Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/3_0.504-1062.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_20762
Length: 1062
Tries: 2!!
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
processing the chunk divide
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
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
...processing 0 of 2
...processing 1 of 2
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1062.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1062.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1062.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1062.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/2_0.0-1062.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1062.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
...processing 0 of 1
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/3_0.504-1062.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/3_0.504-1062.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/3_0.504-1062.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/3_0.504-1062.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/3_0.504-1062.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/3_0.504-1062.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding -5 154 + 0.200 . . . ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_20762
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_20762
examining contents of the fasta file and run log
--Next Contig--
Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/2_0.269-1596.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_20773
Length: 1596
Tries: 2!!
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
processing the chunk divide
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.
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.
annotating transcripts
Making transcripts
...processing 0 of 1
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.269-1596.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.269-1596.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.269-1596.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.269-1596.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/2_0.269-1596.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.269-1596.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding -5 228 + 0.200 . . . ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_20773
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_20773
examining contents of the fasta file and run log
--Next Contig--
Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/2_0.0-1823.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_21504
Length: 1823
Tries: 2!!
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
...processing 0 of 1
...processing 0 of 2
...processing 1 of 2
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1823.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1823.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1823.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1823.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/2_0.0-1823.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1823.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: undefined coordinates
Coding 0 1025 + 0.200 . . . ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_21504
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_21504
examining contents of the fasta file and run log
--Next Contig--
Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/2_0.0-1139.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_21572
Length: 1139
Tries: 2!!
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
...processing 0 of 1
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1139.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1139.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1139.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1139.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/2_0.0-1139.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1139.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: undefined coordinates
Coding 0 760 + 0.200 . . . ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_21572
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_21572
examining contents of the fasta file and run log
--Next Contig--
Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/2_0.0-1068.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_22153
Length: 1068
Tries: 2!!
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
...processing 0 of 1
...processing 0 of 1
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1068.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1068.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1068.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
...processing 0 of 1
running snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1068.AG2-2IIIB.hmm.auto_annotator.xdef.snap /tmp/maker_h0nzdY/0/2_0.0-1068.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1068.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding -7 295 + 0.200 . . . ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_22153
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_22153
examining contents of the fasta file and run log
--Next Contig--
Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/3_0.849-2882.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log
--Next Contig--
Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/14_0.9504-10563.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log
--Next Contig--
Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/4_0.2052-3272.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log
--Next Contig--
Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/5_0.1618-6168.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log
--Next Contig--
Processing run.log file...
examining contents of the fasta file and run log
--Next Contig--
Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/2_0.897-2706.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log
--Next Contig--
Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/6_0.0-4350.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log
--Next Contig--
Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/2_0.0-2576.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log
--Next Contig--
Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/4_0.0-2252.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log
--Next Contig--
Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/3_0.0-1216.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log
--Next Contig--
Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/6_0.5581-6593.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log
--Next Contig--
Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/2_0.106-1764.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log
--Next Contig--
Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/4_0.965-1918.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log
--Next Contig--
Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/2_0.0-1079.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log
--Next Contig--
Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/3_0.504-1062.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log
--Next Contig--
Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/2_0.269-1596.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log
--Next Contig--
Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/2_0.0-1823.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log
--Next Contig--
Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/2_0.0-1139.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log
--Next Contig--
Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/2_0.0-1068.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
Maker is now finished!!!
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